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commit/galaxy-central: jgoecks: Minor curation of data providers: (a) rename gff data provider to match similar providers and (b) add note about how to extend GTF tabix to support GFF/GFF3 as well.
by Bitbucket 24 Apr '12

24 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ea722ae95cb7/ changeset: ea722ae95cb7 user: jgoecks date: 2012-04-24 17:05:47 summary: Minor curation of data providers: (a) rename gff data provider to match similar providers and (b) add note about how to extend GTF tabix to support GFF/GFF3 as well. affected #: 2 files diff -r 562a4f68a4f848bb4be992b27b67fff01ad652c8 -r ea722ae95cb7c99742c081bcd17bddc441dfa2fb lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -1009,9 +1009,9 @@ return { 'data': results, 'message': message } -class GFFDataProvider( TracksDataProvider ): +class RawGFFDataProvider( TracksDataProvider ): """ - Provide data from GFF file. + Provide data from GFF file that has not been indexed. NOTE: this data provider does not use indices, and hence will be very slow for large datasets. @@ -1059,9 +1059,16 @@ return { 'data': results, 'message': message } class GtfTabixDataProvider( TabixDataProvider ): + """ + Returns data from GTF datasets that are indexed via tabix. + """ def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): # Loop through lines and group by transcript_id; each group is a feature. + + # TODO: extend this code or use code in gff_util to process GFF/3 as well + # and then create a generic GFFDataProvider that can be used with both + # raw and tabix datasets. features = {} for count, line in enumerate( iterator ): line_attrs = parse_gff_attributes( line.split('\t')[8] ) diff -r 562a4f68a4f848bb4be992b27b67fff01ad652c8 -r ea722ae95cb7c99742c081bcd17bddc441dfa2fb lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -486,7 +486,7 @@ data = None # TODO: for raw data requests, map dataset type to provider using dict in data_providers.py if isinstance( dataset.datatype, Gff ): - data = GFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) + data = RawGFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' data[ 'extra_info' ] = None elif isinstance( dataset.datatype, Bed ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Add fusion search parameters to Tophat wrapper.
by Bitbucket 24 Apr '12

24 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/562a4f68a4f8/ changeset: 562a4f68a4f8 user: jgoecks date: 2012-04-24 16:35:27 summary: Add fusion search parameters to Tophat wrapper. affected #: 2 files diff -r d01699e14cb0c8edcd4720db2fb6c4b4c284d7e6 -r 562a4f68a4f848bb4be992b27b67fff01ad652c8 tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -58,6 +58,15 @@ parser.add_option( '', '--max-segment-intron', dest='max_segment_intron', help='Maximum intron length that may be found during split-segment search' ) parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' ) parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' ) + + # Fusion search options. + parser.add_option( '', '--fusion-search', action='store_true', dest='fusion_search' ) + parser.add_option( '', '--fusion-anchor-length', dest='fusion_anchor_length' ) + parser.add_option( '', '--fusion-min-dist', dest='fusion_min_dist' ) + parser.add_option( '', '--fusion-read-mismatches', dest='fusion_read_mismatches' ) + parser.add_option( '', '--fusion-multireads', dest='fusion_multireads' ) + parser.add_option( '', '--fusion-multipairs', dest='fusion_multipairs' ) + parser.add_option( '', '--fusion-ignore-chromosomes', dest='fusion_ignore_chromosomes' ) # Wrapper options. parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) @@ -181,13 +190,22 @@ opts += ' --min-segment-intron %d' % int( options.min_segment_intron ) if options.max_segment_intron: opts += ' --max-segment-intron %d' % int( options.max_segment_intron ) + + # Fusion search options. + if options.fusion_search: + opts += ' --fusion-search --fusion-anchor-length %i --fusion-min-dist %i --fusion-read-mismatches %i --fusion-multireads %i --fusion-multipairs %i --fusion-ignore-chromosomes %s' % \ + ( int( options.fusion_anchor_length ), int( options.fusion_min_dist ), + int( options.fusion_read_mismatches ), int( options.fusion_multireads ), + int( options.fusion_multipairs ), options.fusion_ignore_chromosomes ) + cmd = cmd % ( opts, index_path, reads ) + except Exception, e: # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) - #print cmd + print cmd # Run try: @@ -195,7 +213,6 @@ tmp_stdout = open( tmp_out, 'wb' ) tmp_err = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_err, 'wb' ) - print cmd proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr ) returncode = proc.wait() tmp_stderr.close() diff -r d01699e14cb0c8edcd4720db2fb6c4b4c284d7e6 -r 562a4f68a4f848bb4be992b27b67fff01ad652c8 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -83,6 +83,16 @@ #if str($params.microexon_search) == "Yes": --microexon-search #end if + + #if $params.fusion_search.do_search == "Yes": + --fusion-search + --fusion-anchor-length $params.fusion_search.anchor_len + --fusion-min-dist $params.fusion_search.min_dist + --fusion-read-mismatches $params.fusion_search.read_mismatches + --fusion-multireads $params.fusion_search.multireads + --fusion-multipairs $params.fusion_search.multipairs + --fusion-ignore-chromosomes $params.fusion_search.ignore_chromosomes + #end if #end if </command><inputs> @@ -200,10 +210,29 @@ </when><when value="No" /></conditional> + + <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."><option value="No">No</option><option value="Yes">Yes</option></param> + +  + <conditional name="fusion_search"> + <param name="do_search" type="select" label="Do Fusion Search"> + <option selected="true" value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No" /> + <when value="Yes"> + <param name="anchor_len" type="integer" value="20" label="Anchor Length" help="A 'supporting' read must map to both sides of a fusion by at least this many bases."/> + <param name="min_dist" type="integer" value="10000000" label="Minimum Distance" help="For intra-chromosomal fusions, TopHat-Fusion tries to find fusions separated by at least this distance."/> + <param name="read_mismatches" type="integer" value="2" label="Read Mismatches" help="Reads support fusions if they map across fusion with at most this many mismatches."/> + <param name="multireads" type="integer" value="2" label="Multireads" help="Reads that map to more than this many places will be ignored. It may be possible that a fusion is supported by reads (or pairs) that map to multiple places."/> + <param name="multipairs" type="integer" value="2" label="Multipairs" help="Pairs that map to more than this many places will be ignored."/> + <param name="ignore_chromosomes" type="text" value='' label="Ignore some chromosomes such as chrM when detecting fusion break points"/> + </when> + </conditional></when></conditional></inputs> @@ -353,6 +382,14 @@ <param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /><param name="microexon_search" value="Yes" /> +  + <param name="do_search" value="Yes" /> + <param name="anchor_len" value="21" /> + <param name="min_dist" value="10000021" /> + <param name="read_mismatches" value="3" /> + <param name="multireads" value="4" /> + <param name="multipairs" value="5" /> + <param name="ignore_chromosomes" value="chrM"/><output name="insertions" file="tophat_out3i.bed" /><output name="deletions" file="tophat_out3d.bed" /><output name="junctions" file="tophat_out3j.bed" /> @@ -390,6 +427,14 @@ <param name="no_novel_juncs" value="No" /><param name="use_search" value="No" /><param name="microexon_search" value="Yes" /> +  + <param name="do_search" value="Yes" /> + <param name="anchor_len" value="21" /> + <param name="min_dist" value="10000021" /> + <param name="read_mismatches" value="3" /> + <param name="multireads" value="4" /> + <param name="multipairs" value="5" /> + <param name="ignore_chromosomes" value="chrM"/><output name="junctions" file="tophat_out4j.bed" /><output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" /></test> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Enhance the "find workflows" feature in the tool shed and installe dtool shed repositories to allow for finding all workflows if the search criteria is blank.
by Bitbucket 23 Apr '12

23 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d01699e14cb0/ changeset: d01699e14cb0 user: greg date: 2012-04-23 21:59:04 summary: Enhance the "find workflows" feature in the tool shed and installe dtool shed repositories to allow for finding all workflows if the search criteria is blank. affected #: 2 files diff -r 98f47fbe0a4f289e7078d5f0aab1c03caeeedf49 -r d01699e14cb0c8edcd4720db2fb6c4b4c284d7e6 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -475,13 +475,16 @@ # This can only occur when there is a multi-select grid with check boxes and an operation, # and the user clicked the operation button without checking any of the check boxes. return trans.show_error_message( "No items were selected." ) - workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ] - exact_matches = params.get( 'exact_matches', '' ) - exact_matches_checked = CheckboxField.is_checked( exact_matches ) - match_tuples = [] - ok = True - if workflow_names: - ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) + if 'find_workflows_button' in kwd: + workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ] + exact_matches = params.get( 'exact_matches', '' ) + exact_matches_checked = CheckboxField.is_checked( exact_matches ) + match_tuples = [] + ok = True + if workflow_names: + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) + else: + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view @@ -506,6 +509,9 @@ else: message = "No search performed - each field must contain the same number of comma-separated items." status = "error" + else: + exact_matches_checked = False + workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/community/repository/find_workflows.mako', webapp=webapp, @@ -593,7 +599,7 @@ exact_matches_check_box=exact_matches_check_box, message=message, status=status ) - def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='' ): + def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): match_tuples = [] ok = True for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): @@ -661,6 +667,8 @@ for workflow_name in workflow_names: if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif all_workflows and 'workflows' in metadata: + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return ok, match_tuples def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ): workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() diff -r 98f47fbe0a4f289e7078d5f0aab1c03caeeedf49 -r d01699e14cb0c8edcd4720db2fb6c4b4c284d7e6 templates/webapps/community/repository/find_workflows.mako --- a/templates/webapps/community/repository/find_workflows.mako +++ b/templates/webapps/community/repository/find_workflows.mako @@ -26,7 +26,7 @@ <div class="toolFormTitle">Search repositories for workflows</div><div class="toolFormBody"><div class="form-row"> - Enter a workflow name to find repositories that contain workflows matching the search criteria.<br/><br/> + Enter a workflow name to find repositories that contain workflows matching the search criteria, or leave blank to find all repositories that contain a workflow.<br/><br/> Comma-separated strings may be entered to expand search criteria. </div><div style="clear: both"></div> @@ -46,7 +46,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <input type="submit" value="Search repositories"/> + <input type="submit" name="find_workflows_button" value="Search repositories"/></div></form></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Update Trinity wrapper to support most recent versions.
by Bitbucket 23 Apr '12

23 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/98f47fbe0a4f/ changeset: 98f47fbe0a4f user: jgoecks date: 2012-04-23 21:29:37 summary: Update Trinity wrapper to support most recent versions. affected #: 1 file diff -r 6d551feac6c0780979a1ce551a5430990473d864 -r 98f47fbe0a4f289e7078d5f0aab1c03caeeedf49 tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -1,5 +1,5 @@ <tool id="trinity_all" name="Trinity" version="0.0.1"> -  + <description>De novo assembly of RNA-Seq data</description><requirements><requirement type="package">trinity</requirement> @@ -35,8 +35,10 @@ #end if #end if + --kmer_method meryl + ## CPU and butterfly options. - --CPU 4 --run_butterfly --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 + --CPU 4 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 </command><inputs><conditional name="inputs"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: More fixes for retrieving updates for an installed tool shed repository.
by Bitbucket 23 Apr '12

23 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6d551feac6c0/ changeset: 6d551feac6c0 user: greg date: 2012-04-23 20:50:27 summary: More fixes for retrieving updates for an installed tool shed repository. affected #: 1 file diff -r dd44d4e5219a279400a56825b2ff6e2e81683c98 -r 6d551feac6c0780979a1ce551a5430990473d864 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -876,6 +876,7 @@ repository = get_repository_by_name_and_owner( trans, name, owner ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) + latest_ctx = get_changectx_for_changeset( repo, changeset_revision ) from_update_manager = webapp == 'update_manager' if from_update_manager: update = 'true' @@ -889,6 +890,7 @@ # If changeset_revision is the repository tip, we know there are no additional updates for the tools. if from_update_manager: return no_update + # Return the same value for changeset_revision and latest_changeset_revision. url += repository.tip else: repository_metadata = get_repository_metadata_by_changeset_revision( trans, @@ -902,9 +904,6 @@ else: # Return the same value for changeset_revision and latest_changeset_revision. url += changeset_revision - # Get the ctx_rev for the changeset_revision. - latest_ctx = get_changectx_for_changeset( repo, changeset_revision ) - url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) else: # The changeset_revision column in the repository_metadata table has been # updated with a new changeset_revision value since the repository was cloned. @@ -965,7 +964,6 @@ url += repository_metadata.changeset_revision # Get the ctx_rev for the discovered changeset_revision. latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) found = True break if not found: @@ -979,6 +977,7 @@ if from_update_manager: return no_update url += changeset_revision + url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) return trans.response.send_redirect( url ) @web.expose def browse_repositories( self, trans, **kwd ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for getting updates to an installed tool shed repository where no updates are available.
by Bitbucket 23 Apr '12

23 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dd44d4e5219a/ changeset: dd44d4e5219a user: greg date: 2012-04-23 20:19:42 summary: Fix for getting updates to an installed tool shed repository where no updates are available. affected #: 1 file diff -r 476ce0b78713d5b42ef3e7f6e09b8450496a3692 -r dd44d4e5219a279400a56825b2ff6e2e81683c98 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -874,6 +874,8 @@ changeset_revision = params.get( 'changeset_revision', None ) webapp = params.get( 'webapp', 'community' ) repository = get_repository_by_name_and_owner( trans, name, owner ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) from_update_manager = webapp == 'update_manager' if from_update_manager: update = 'true' @@ -884,8 +886,7 @@ url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( repository.name, repository.user.username, changeset_revision ) if changeset_revision == repository.tip: - # If changeset_revision is the repository tip, then - # we know there are no additional updates for the tools. + # If changeset_revision is the repository tip, we know there are no additional updates for the tools. if from_update_manager: return no_update url += repository.tip @@ -898,12 +899,15 @@ # repository, then we know there are no additional updates for the tools. if from_update_manager: return no_update - url += changeset_revision + else: + # Return the same value for changeset_revision and latest_changeset_revision. + url += changeset_revision + # Get the ctx_rev for the changeset_revision. + latest_ctx = get_changectx_for_changeset( repo, changeset_revision ) + url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) else: # The changeset_revision column in the repository_metadata table has been # updated with a new changeset_revision value since the repository was cloned. - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) # Load each tool in the repository's changeset_revision to generate a list of # tool guids, since guids differentiate tools by id and version. ctx = get_changectx_for_changeset( repo, changeset_revision ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix the tasks runner that I broke when I split job management into multiple processes.
by Bitbucket 23 Apr '12

23 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/476ce0b78713/ changeset: 476ce0b78713 user: natefoo date: 2012-04-23 20:04:45 summary: Fix the tasks runner that I broke when I split job management into multiple processes. affected #: 1 file diff -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 -r 476ce0b78713d5b42ef3e7f6e09b8450496a3692 lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -83,7 +83,7 @@ for task in tasks: tw = TaskWrapper(task, job_wrapper.queue) task_wrappers.append(tw) - self.app.job_manager.dispatcher.put(tw) + self.app.job_manager.job_handler.dispatcher.put(tw) tasks_incomplete = False count_complete = 0 sleep_time = 1 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Provide mercurial as an egg for tool shed operations.
by Bitbucket 23 Apr '12

23 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c8f4f73e9199/ changeset: c8f4f73e9199 user: natefoo date: 2012-04-23 19:20:29 summary: Provide mercurial as an egg for tool shed operations. affected #: 10 files diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 dist-eggs.ini --- a/dist-eggs.ini +++ b/dist-eggs.ini @@ -7,105 +7,82 @@ ; [hosts] -py2.4-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.4 -py2.4-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.4 py2.5-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.5 py2.5-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.5 py2.6-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.6 py2.6-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.6 py2.7-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.7 py2.7-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.7 -py2.4-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.4 -py2.4-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.4 py2.5-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.5 py2.5-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5 py2.6-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.6 py2.6-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 py2.7-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.7 py2.7-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 -py2.4-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /usr/local/bin/python2.4 -py2.5-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /usr/local/bin/python2.5 -py2.6-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /usr/local/bin/python2.6 -py2.7-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /usr/local/bin/python2.7 +py2.5-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.5/bin/python2.5 +py2.6-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 +py2.7-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 py2.6-macosx-10.6-universal-ucs2 = lion.bx.psu.edu /usr/bin/python2.6 py2.7-macosx-10.6-intel-ucs2 = lion.bx.psu.edu /usr/local/bin/python2.7 -py2.4-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6 py2.7-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.7 -py2.4-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.6 py2.7-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.7 -py2.4-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.4 py2.5-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 py2.6-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 py2.7-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.7 -py2.4-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.4 -py2.5-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.5 -py2.6-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.6 -py2.7-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.7 +py2.5-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.5 +py2.6-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.6 +py2.7-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.7 ; these hosts are used to build eggs with no C extensions -py2.4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.4 py2.5 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5 py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 py2.7 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 [groups] -py2.4-linux-i686 = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 -py2.4-linux-x86_64 = py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 py2.5-linux-i686 = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64 = py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-i686 = py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.6-linux-x86_64 = py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.7-linux-i686 = py2.7-linux-i686-ucs2 py2.7-linux-i686-ucs4 py2.7-linux-x86_64 = py2.7-linux-x86_64-ucs2 py2.7-linux-x86_64-ucs4 -py2.4-linux = py2.4-linux-i686 py2.4-linux-x86_64 py2.5-linux = py2.5-linux-i686 py2.5-linux-x86_64 py2.6-linux = py2.6-linux-i686 py2.6-linux-x86_64 py2.7-linux = py2.7-linux-i686 py2.7-linux-x86_64 -linux-i686 = py2.4-linux-i686 py2.5-linux-i686 py2.6-linux-i686 py2.7-linux-i686 -linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 py2.6-linux-x86_64 py2.7-linux-x86_64 +linux-i686 = py2.5-linux-i686 py2.6-linux-i686 py2.7-linux-i686 +linux-x86_64 = py2.5-linux-x86_64 py2.6-linux-x86_64 py2.7-linux-x86_64 linux = linux-i686 linux-x86_64 -py2.4-macosx = py2.4-macosx-10.3-fat-ucs2 py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.7-macosx = py2.7-macosx-10.3-fat-ucs2 py2.7-macosx-10.6-intel-ucs2 -macosx = py2.4-macosx py2.5-macosx py2.6-macosx py2.7-macosx -py2.4-solaris-i86pc = py2.4-solaris-2.10-i86pc_32-ucs2 py2.4-solaris-2.10-i86pc_64-ucs2 +macosx = py2.5-macosx py2.6-macosx py2.7-macosx py2.5-solaris-i86pc = py2.5-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-i86pc = py2.6-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.7-solaris-i86pc = py2.7-solaris-2.10-i86pc_32-ucs2 py2.7-solaris-2.10-i86pc_64-ucs2 -py2.4-solaris-sun4u = py2.4-solaris-2.10-sun4u_32-ucs2 py2.4-solaris-2.10-sun4u_64-ucs2 py2.5-solaris-sun4u = py2.5-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-sun4u = py2.6-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 py2.7-solaris-sun4u = py2.7-solaris-2.10-sun4u_32-ucs2 py2.7-solaris-2.10-sun4u_64-ucs2 -py2.4-solaris = py2.4-solaris-i86pc py2.4-solaris-sun4u py2.5-solaris = py2.5-solaris-i86pc py2.5-solaris-sun4u py2.6-solaris = py2.6-solaris-i86pc py2.6-solaris-sun4u py2.7-solaris = py2.7-solaris-i86pc py2.7-solaris-sun4u -solaris-i86pc = py2.4-solaris-i86pc py2.5-solaris-i86pc py2.6-solaris-i86pc py2.7-solaris-i86pc -solaris-sun4u = py2.4-solaris-sun4u py2.5-solaris-sun4u py2.6-solaris-sun4u py2.7-solaris-sun4u +solaris-i86pc = py2.5-solaris-i86pc py2.6-solaris-i86pc py2.7-solaris-i86pc +solaris-sun4u = py2.5-solaris-sun4u py2.6-solaris-sun4u py2.7-solaris-sun4u solaris = solaris-i86pc solaris-sun4u -py2.4-all = py2.4-linux py2.4-macosx py2.4-solaris py2.5-all = py2.5-linux py2.5-macosx py2.5-solaris py2.6-all = py2.6-linux py2.6-macosx py2.6-solaris py2.7-all = py2.7-linux py2.7-macosx py2.7-solaris -; group for building pysam on solaris 10 sparc -;solaris-2.10-sun4u = py2.4-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.4-solaris-2.10-sun4u_64-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 - ; the 'all' key is used internally by the build system to specify which hosts ; to build on when no hosts are specified on the dist-eggs.py command line. all = linux macosx solaris ; the 'noplatform' key, likewise, is for which build hosts should be used when ; building pure python (noplatform) eggs. -noplatform = py2.4 py2.5 py2.6 py2.7 +noplatform = py2.5 py2.6 py2.7 ; don't build these eggs on these platforms: [ignore] -GeneTrack = py2.4 -python-daemon = py2.4 ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.7-linux-i686-ucs2 py2.7-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.7-linux-x86_64-ucs2 py2.7-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.7-macosx-10.3-fat-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.7-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.7-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.7-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 py2.7-solaris-2.10-sun4u_64-ucs2 diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -17,6 +17,7 @@ ctypes = 1.0.2 DRMAA_python = 0.2 MarkupSafe = 0.12 +mercurial = 2.1.2 MySQL_python = 1.2.3c1 numpy = 1.6.0 pbs_python = 4.1.0 diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -6,6 +6,8 @@ from galaxy.util.json import * from galaxy.tools.search import ToolBoxSearch from galaxy.model.orm import * + +pkg_resources.require( 'mercurial' ) from mercurial import ui, commands pkg_resources.require( 'elementtree' ) diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -2,7 +2,9 @@ from galaxy.web.controllers.admin import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * -from galaxy import tools +from galaxy import eggs, tools + +eggs.require( 'mercurial' ) from mercurial import hg log = logging.getLogger( __name__ ) diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -6,7 +6,11 @@ from galaxy.util.shed_util import get_configured_ui from common import * from repository import RepositoryListGrid, CategoryListGrid + +from galaxy import eggs +eggs.require('mercurial') from mercurial import hg + import logging log = logging.getLogger( __name__ ) diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -11,6 +11,9 @@ from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.model.item_attrs import UsesItemRatings + +from galaxy import eggs +eggs.require('mercurial') from mercurial import hg, ui, commands log = logging.getLogger( __name__ ) diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -1,6 +1,9 @@ import os, logging from galaxy.web.base.controller import * from galaxy.webapps.community.controllers.common import * + +from galaxy import eggs +eggs.require('mercurial') from mercurial.hgweb.hgwebdir_mod import hgwebdir from mercurial.hgweb.request import wsgiapplication diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -12,6 +12,9 @@ from galaxy.model.orm import * from galaxy.util.shed_util import get_configured_ui from common import * + +from galaxy import eggs +eggs.require('mercurial') from mercurial import hg, ui, patch, commands log = logging.getLogger( __name__ ) diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -4,6 +4,9 @@ from galaxy.datatypes.checkers import * from common import * from galaxy.util.shed_util import get_configured_ui, handle_sample_tool_data_table_conf_file + +from galaxy import eggs +eggs.require('mercurial') from mercurial import hg, ui, commands log = logging.getLogger( __name__ ) diff -r 18c426204a337f94377074afa863261b6a4b10be -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -9,7 +9,11 @@ from galaxy.util.bunch import Bunch from galaxy.util.hash_util import * from galaxy.web.form_builder import * + +from galaxy import eggs +eggs.require('mercurial') from mercurial import hg, ui + log = logging.getLogger( __name__ ) class User( object ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Better message when creating a custom build.
by Bitbucket 23 Apr '12

23 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/18c426204a33/ changeset: 18c426204a33 user: jgoecks date: 2012-04-23 17:24:46 summary: Better message when creating a custom build. affected #: 1 file diff -r ebd5932ed7f1d0b434383995ea1338609b9814f4 -r 18c426204a337f94377074afa863261b6a4b10be templates/user/dbkeys.mako --- a/templates/user/dbkeys.mako +++ b/templates/user/dbkeys.mako @@ -149,7 +149,7 @@ % if 'count' in dct: ${dct['count']} % else: - ? + Processing % endif </td><td><form action="dbkeys" method="post"><input type="hidden" name="key" value="${key}" /><input type="submit" name="delete" value="Delete" /></form></td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 23 Apr '12

23 Apr '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c5da9bd8bbfc/ changeset: c5da9bd8bbfc user: jgoecks date: 2012-04-23 15:08:29 summary: Use tabix for indexing and getting data from GTF files. This is faster and more flexible than using interval index. affected #: 3 files diff -r 8b773372d0dce1d815b90d257efa073d5a039e72 -r c5da9bd8bbfc1e2634b7981c836a62796f7b33f7 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -85,7 +85,11 @@ <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/><datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/><datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/> - <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/> + <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"> + <converter file="gff_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="gff_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + </datatype><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /><datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/><datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"> diff -r 8b773372d0dce1d815b90d257efa073d5a039e72 -r c5da9bd8bbfc1e2634b7981c836a62796f7b33f7 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -953,6 +953,9 @@ dataset.metadata.attribute_types = attribute_types dataset.metadata.attributes = len( attribute_types ) Gff.set_meta( self, dataset, overwrite = overwrite, skip = i ) + + def get_track_type( self ): + return "FeatureTrack", {"data": "tabix", "index": "summary_tree"} class Wiggle( Tabular, _RemoteCallMixin ): diff -r 8b773372d0dce1d815b90d257efa073d5a039e72 -r c5da9bd8bbfc1e2634b7981c836a62796f7b33f7 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -1024,7 +1024,7 @@ """ start, end = int( start ), int( end ) source = open( self.original_dataset.file_name ) - + def features_in_region_iter(): offset = 0 for feature in GFFReaderWrapper( source, fix_strand=True ): @@ -1034,7 +1034,7 @@ yield feature, offset offset += feature.raw_size return features_in_region_iter() - + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ Process data from an iterator to a format that can be provided to client. @@ -1057,6 +1057,47 @@ return { 'data': results, 'message': message } + +class GtfTabixDataProvider( TabixDataProvider ): + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + # Loop through lines and group by transcript_id; each group is a feature. + features = {} + for count, line in enumerate( iterator ): + line_attrs = parse_gff_attributes( line.split('\t')[8] ) + transcript_id = line_attrs[ 'transcript_id' ] + if transcript_id in features: + feature = features[ transcript_id ] + else: + feature = [] + features[ transcript_id ] = feature + feature.append( line ) + + # Set up iterator for features. + def features_iterator(): + for transcript_id, feature in features.items(): + for line in feature: + yield line + + # Process data. + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + results = [] + message = None + + # TODO: remove reader-wrapper and create features directly. + for count, feature in enumerate( GFFReaderWrapper( features_iterator() ) ): + if count < start_val: + continue + if count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "reads" ) + break + + payload = package_gff_feature( feature, no_detail=no_detail, filter_cols=filter_cols ) + payload.insert( 0, feature.intervals[ 0 ].attributes[ 'transcript_id' ] ) + results.append( payload ) + + return { 'data': results, 'message': message } # # -- ENCODE Peak data providers. @@ -1189,6 +1230,7 @@ "tabix": { Vcf: VcfTabixDataProvider, Bed: BedTabixDataProvider, + Gtf: GtfTabixDataProvider, ENCODEPeak: ENCODEPeakTabixDataProvider, Interval: IntervalTabixDataProvider, "default" : TabixDataProvider }, https://bitbucket.org/galaxy/galaxy-central/changeset/678ac108a4c4/ changeset: 678ac108a4c4 user: jgoecks date: 2012-04-23 15:28:12 summary: Fix style conflict between base.css and trackster.css affected #: 5 files diff -r c5da9bd8bbfc1e2634b7981c836a62796f7b33f7 -r 678ac108a4c44b06693a22f6d7d301986a3b30f3 static/june_2007_style/base_sprites.less.tmpl --- a/static/june_2007_style/base_sprites.less.tmpl +++ b/static/june_2007_style/base_sprites.less.tmpl @@ -88,6 +88,10 @@ } .icon-button.plus-button { -sprite-group: fugue; + -sprite-image: fugue/plus-button-bw.png; +} +.icon-button.plus-button:hover { + -sprite-group: fugue; -sprite-image: fugue/plus-button.png; } .icon-button.gear { diff -r c5da9bd8bbfc1e2634b7981c836a62796f7b33f7 -r 678ac108a4c44b06693a22f6d7d301986a3b30f3 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -751,9 +751,10 @@ .icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -286px;} .icon-button.import{background:url(fugue.png) no-repeat 0px -312px;} .icon-button.plus-button{background:url(fugue.png) no-repeat 0px -338px;} -.icon-button.gear{background:url(fugue.png) no-repeat 0px -364px;} -.icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -390px;} -.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -416px;} +.icon-button.plus-button:hover{background:url(fugue.png) no-repeat 0px -364px;} +.icon-button.gear{background:url(fugue.png) no-repeat 0px -390px;} +.icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -416px;} +.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -442px;} div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} diff -r c5da9bd8bbfc1e2634b7981c836a62796f7b33f7 -r 678ac108a4c44b06693a22f6d7d301986a3b30f3 static/june_2007_style/blue/fugue.png Binary file static/june_2007_style/blue/fugue.png has changed diff -r c5da9bd8bbfc1e2634b7981c836a62796f7b33f7 -r 678ac108a4c44b06693a22f6d7d301986a3b30f3 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -86,8 +86,6 @@ .icon-button.toggle-expand:hover{background:transparent url(../images/fugue/toggle-expand.png) no-repeat;} .icon-button.cross-circle{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;} .icon-button.cross-circle:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} -.icon-button.plus-button{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;} -.icon-button.plus-button:hover{background:transparent url(../images/fugue/plus-button.png) no-repeat;} .icon-button.block--plus{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;} .icon-button.block--plus:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;} .icon-button.bookmarks{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;} diff -r c5da9bd8bbfc1e2634b7981c836a62796f7b33f7 -r 678ac108a4c44b06693a22f6d7d301986a3b30f3 static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -411,12 +411,6 @@ .icon-button.cross-circle:hover { background: transparent url(../images/fugue/cross-circle.png) no-repeat; } -.icon-button.plus-button { - background: transparent url(../images/fugue/plus-button-bw.png) no-repeat; -} -.icon-button.plus-button:hover { - background: transparent url(../images/fugue/plus-button.png) no-repeat; -} .icon-button.block--plus { background: transparent url(../images/fugue/block--plus-bw.png) no-repeat; } https://bitbucket.org/galaxy/galaxy-central/changeset/ebd5932ed7f1/ changeset: ebd5932ed7f1 user: jgoecks date: 2012-04-23 17:14:27 summary: Create GTF features directly rather than parsing from lines. This is much faster than parsing. affected #: 2 files diff -r 678ac108a4c44b06693a22f6d7d301986a3b30f3 -r ebd5932ed7f1d0b434383995ea1338609b9814f4 lib/galaxy/datatypes/util/gff_util.py --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -10,8 +10,8 @@ A GFF interval, including attributes. If file is strictly a GFF file, only attribute is 'group.' """ - def __init__( self, reader, fields, chrom_col, feature_col, start_col, end_col, \ - strand_col, score_col, default_strand, fix_strand=False ): + def __init__( self, reader, fields, chrom_col=0, feature_col=2, start_col=3, end_col=4, \ + strand_col=6, score_col=5, default_strand='.', fix_strand=False ): # HACK: GFF format allows '.' for strand but GenomicInterval does not. To get around this, # temporarily set strand and then unset after initing GenomicInterval. unknown_strand = False @@ -45,8 +45,8 @@ """ A GFF feature, which can include multiple intervals. """ - def __init__( self, reader, chrom_col, feature_col, start_col, end_col, \ - strand_col, score_col, default_strand, fix_strand=False, intervals=[], \ + def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4, \ + strand_col=6, score_col=5, default_strand='.', fix_strand=False, intervals=[], \ raw_size=0 ): GFFInterval.__init__( self, reader, intervals[0].fields, chrom_col, feature_col, \ start_col, end_col, strand_col, score_col, default_strand, \ diff -r 678ac108a4c44b06693a22f6d7d301986a3b30f3 -r ebd5932ed7f1d0b434383995ea1338609b9814f4 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -1071,28 +1071,22 @@ else: feature = [] features[ transcript_id ] = feature - feature.append( line ) - - # Set up iterator for features. - def features_iterator(): - for transcript_id, feature in features.items(): - for line in feature: - yield line - + feature.append( GFFInterval( None, line.split( '\t') ) ) + # Process data. filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) results = [] message = None - # TODO: remove reader-wrapper and create features directly. - for count, feature in enumerate( GFFReaderWrapper( features_iterator() ) ): + for count, intervals in enumerate( features.values() ): if count < start_val: continue if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "reads" ) break - + + feature = GFFFeature( None, intervals=intervals ) payload = package_gff_feature( feature, no_detail=no_detail, filter_cols=filter_cols ) payload.insert( 0, feature.intervals[ 0 ].attributes[ 'transcript_id' ] ) results.append( payload ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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